rs1360180

Positions:

• chr1-68246675-G-A
• chr1-68246675-G-C

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.108 in 152,032 control chromosomes in the GnomAD database, including 1,025 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.11 (1025 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.87).
• BA1: GnomAd4 highest subpopulation (AMR) allele frequency at 95% confidence interval = 0.17 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	MANE	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	#exon/exons	TSL	MANE	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.108 AC: 16444 AN: 151914 Hom.: 1022 Cov.: 32

Gnomad AFR AF: 0.0675

Gnomad AMI AF: 0.0735

Gnomad AMR AF: 0.176

Gnomad ASJ AF: 0.128

Gnomad EAS AF: 0.0869

Gnomad SAS AF: 0.156

Gnomad FIN AF: 0.0714

Gnomad MID AF: 0.161

Gnomad NFE AF: 0.120

Gnomad OTH AF: 0.130

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.108 AC: 16436 AN: 152032 Hom.: 1025 Cov.: 32 AF XY: 0.108 AC XY: 8062 AN XY: 74310

Gnomad4 AFR AF: 0.0674

Gnomad4 AMR AF: 0.176

Gnomad4 ASJ AF: 0.128

Gnomad4 EAS AF: 0.0873

Gnomad4 SAS AF: 0.155

Gnomad4 FIN AF: 0.0714

Gnomad4 NFE AF: 0.120

Gnomad4 OTH AF: 0.128

Alfa AF: 0.122 Hom.: 1615

Bravo AF: 0.114

Asia WGS AF: 0.0980 AC: 343 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.87
CADD	Benign	5.4
DANN	Benign	0.73

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs1360180; hg19: chr1-68712358;